[Bioperl-l] Bio::SearchIO blastxml for multiple queries

Jay Konieczka jayk at u.arizona.edu
Wed Mar 14 00:15:25 EDT 2007


My blastxml output, which is supposed to contain multiple queries,  
each having multiple hits, is improperly parsed by Bio::SearchIO -  
only the first query is recognized.  I realize there has been plenty  
of talk about this issue since it arose, but I've been having trouble  
finding instructions for a patch.  Is there an easy fix for this?    
I'm running blastall version 2.2.15 (using blastn) and attempting to  
parse the output with bioperl 1.4.

Thanks for any help,


Jay H. Konieczka
Ph.D. Student, Antin Lab
Molecular & Cellular Biology
University of Arizona

Phone:  1.520.591.3446

1656 E. Mabel, MRB 317
Tucson, AZ 85724 USA

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